Cura Dual Material Merge problems

We have just installed a new Dual Extruder Head for our TAZ4 3d Printer.
We can get the test object to print OK.
We are now trying to design objects using 2 colors of ABS.
We can get only aprox. 50% of our designs to Merge correctly !
See Screen Capture#1 for the 2 original objects & Screen Capture#2 for correct Dual Material Merge results.
See Screen Capture#3 for the 2 original objects & Screen Capture#4 for INCORRECT Dual Material Merge results.
We were suprised that changing just the text size would cause this problem.
Thanks in advance for any help, ideas and suggestions.

That is bizarre. Care to post the files themselves? There must be some difference in configuration that is causing the different behavior. Are they all generated from the same computer and design program? Is there any pattern behind how the parts that do not align correctly were created? How many design attempts are we talking about here 2-3 or much more?

FYI there is a much newer version of Cura now (v17) get it from here:

If you move the two pieces of the model out of alignment relative to each other on the CAD build platform, they will merge in the same relative positions in Cura as well. At least that’s the case for Tinkercad and Sketchup, I’ve not had a chance to test others.
Try re-aligning the parts in your CAD software, then re-save the .stls for merging in CURA.

I had this problem to and it was right that the 2 models were out of alignment. They must be in the same location relative to the origin on the CAD file as said above.

I have a model of a wheel that I cut the center out and “saved as” and then cut the same off the outer to have a flexible wheel with a solid hub, Its literally the same part with same origin on the same plane. Its dimensions fit perfectly to the diameter of the cut. (see pic).
The do not align. I have a number of parts that are saving this way but have no idea why!
I have not been able to print a model Ive created. The test prints align perfectly. I read the previous replies. Any one else have ant other hints?

Heres another view


What software are you using to create the models?